Abstract:
BACKGROUND:Typhoid fever is an infectious disease of global importance that is caused by Salmonella enterica subsp. enterica serovar Typhi (S. Typhi). This disease causes an estimated 200,000 deaths per year and remains a serious global health threat. S. Typhi is strictly a human pathogen, and some recovered individuals become long-term carriers who continue to shed the bacteria in their faeces, thus becoming main reservoirs of infection. RESULTS:A comparative genomics analysis combined with a phylogenomic analysis revealed that the strains from the outbreak and carrier were closely related with microvariations and possibly derived from a common ancestor. Additionally, the comparative genomics analysis with all of the other completely sequenced S. Typhi genomes revealed that strains BL196 and CR0044 exhibit unusual genomic variations despite S. Typhi being generally regarded as highly clonal. The two genomes shared distinct chromosomal architectures and uncommon genome features; notably, the presence of a ~10 kb novel genomic island containing uncharacterised virulence-related genes, and zot in particular. Variations were also detected in the T6SS system and genes that were related to SPI-10, insertion sequences, CRISPRs and nsSNPs among the studied genomes. Interestingly, the carrier strain CR0044 harboured far more genetic polymorphisms (83% mutant nsSNPs) compared with the closely related BL196 outbreak strain. Notably, the two highly related virulence-determinant genes, rpoS and tviE, were mutated in strains BL196 and CR0044, respectively, which revealed that the mutation in rpoS is stabilising, while that in tviE is destabilising. These microvariations provide novel insight into the optimisation of genes by the pathogens. However, the sporadic strain was found to be far more conserved compared with the others. CONCLUSIONS:The uncommon genomic variations in the two closely related BL196 and CR0044 strains suggests that S. Typhi is more diverse than previously thought. Our study has demonstrated that the pathogen is continually acquiring new genes through horizontal gene transfer in the process of host adaptation, providing novel insight into its unusual genomic dynamics. The understanding of these strains and virulence factors, and particularly the strain that is associated with the large outbreak and the less studied asymptomatic Typhi carrier in the population, will have important impact on disease control.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Yap KP,Gan HM,Teh CS,Chai LC,Thong KLdoi
10.1186/1471-2164-15-1007subject
Has Abstractpub_date
2014-11-20 00:00:00pages
1007issn
1471-2164pii
1471-2164-15-1007journal_volume
15pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Atlantic salmon production in Tasmania (Southern Australia) occurs near the upper limits of the species thermal tolerance. Summer water temperatures can average over 19 °C over several weeks and have negative effects on performance and health. Liver tissue exerts important metabolic functions in thermal adap...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4517-0
更新日期:2018-02-12 00:00:00
abstract:BACKGROUND:Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3457-9
更新日期:2017-01-10 00:00:00
abstract:BACKGROUND:In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation. To understand the molecular mechanism of how productive bidirectional transcription is r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4697-7
更新日期:2018-05-02 00:00:00
abstract:BACKGROUND:Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-222
更新日期:2006-08-31 00:00:00
abstract:BACKGROUND:Two fifths of the world's population is at risk from dengue. The absence of effective drugs and vaccines leaves vector control as the primary intervention tool. Understanding dengue virus (DENV) host interactions is essential for the development of novel control strategies. The availability of genome sequenc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-380
更新日期:2010-06-16 00:00:00
abstract:BACKGROUND:The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly anal...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-537
更新日期:2013-08-08 00:00:00
abstract:BACKGROUND:Ser/Thr/Tyr kinases (STYKs) commonly found in eukaryotes have been recently reported in many bacterial species. Recent studies elucidating their cellular functions have established their roles in bacterial growth and development. However functions of a large number of bacterial STYKs still remain elusive. Th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-129
更新日期:2005-09-19 00:00:00
abstract:BACKGROUND:Sequencing of the approximately 1.7 billion bases of the zebrafish genome is currently underway. To date, few high resolution genetic maps exist for the zebrafish genome, based mainly on single nucleotide polymorphisms (SNPs) and short microsatellite repeats. The desire to construct a higher resolution genet...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-347
更新日期:2010-06-01 00:00:00
abstract:BACKGROUND:The cotton (Gossypium spp.) fiber cell is an important unicellular model for studying cell differentiation. There is evidence suggesting that phosphorylation is a critical post-translational modification involved in regulation of a wide range of cell activities. Nevertheless, the sites of phosphorylation in ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-466
更新日期:2014-06-12 00:00:00
abstract:BACKGROUND:The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we inve...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-511
更新日期:2011-10-17 00:00:00
abstract:BACKGROUND:Embryonic and fetal exposure to maternal obesity causes several maladaptive morphological and epigenetic changes in exposed offspring. The timing of these events is unclear, but changes can be observed even after a short exposure to maternal obesity around the time of conception. The hypothesis of this work ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5120-0
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-5-28
更新日期:2004-04-29 00:00:00
abstract:BACKGROUND:Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-347
更新日期:2013-05-24 00:00:00
abstract::The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the billions of base-pairs of Archosaur sequence that have become available in the last few years. This editorial de...
journal_title:BMC genomics
pub_type:
doi:10.1186/1471-2164-10-S2-I1
更新日期:2009-07-14 00:00:00
abstract:BACKGROUND:Rice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provides ample opportunities to understand the molecular mechanism of its pathogenesis on rice plants a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-310
更新日期:2006-12-08 00:00:00
abstract:BACKGROUND:Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adoption of these physiological systems as molecular model systems. In this study, we sequenced and perfo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3215-z
更新日期:2016-11-04 00:00:00
abstract:BACKGROUND:Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not annotated) variation, is problematic for follow up analyses. Polymorphisms result in a high inciden...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-379
更新日期:2009-08-17 00:00:00
abstract:BACKGROUND:The occurrence of liver cancer is higher in males than in females, and the incidence increases during aging. Signaling pathways regulated by retinoid x receptor alpha (RXRalpha) are involved in hepatocellular carcinogenesis. The phenotype of hepatocyte RXRalpha deficient mice is different between genders. To...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-403
更新日期:2008-08-28 00:00:00
abstract:BACKGROUND:The histone variant H2A.Z, which has been reported to have both activating and repressive effects on gene expression, is known to occupy nucleosomes at the 5' ends of protein-coding genes. RESULTS:We now find that H2A.Z is also significantly enriched in gene coding regions and at the 3' ends of genes in bud...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1247-4
更新日期:2015-02-19 00:00:00
abstract:BACKGROUND:The transcription factor SOX10 is essential for all stages of Schwann cell development including myelination. SOX10 cooperates with other transcription factors to activate the expression of key myelin genes in Schwann cells and is therefore a context-dependent, pro-myelination transcription factor. As such, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3167-3
更新日期:2016-11-07 00:00:00
abstract:BACKGROUND:Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this deterioration. Eggshell formation is a highly complex process under precise regulation of genes and bio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07177-7
更新日期:2020-11-09 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play versatile roles in plants, functioning in processes such as growth, development and stress responses. Chilling is a common abiotic stress that seriously ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1130
更新日期:2014-12-17 00:00:00
abstract:BACKGROUND:Microarray data analysts commonly filter out genes based on a number of ad hoc criteria prior to any high-level statistical analysis. Such ad hoc approaches could lead to conflicting conclusions with no clear guidance as to which method is most likely to be reproducible. Furthermore, the number of tests perf...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-33
更新日期:2006-02-22 00:00:00
abstract:BACKGROUND:Sweet sorghum is an annual C4 crop considered to be one of the most promising bio-energy crops due to its high sugar content in stem, yet it is poorly understood how this plant increases its sugar content in response to salt stress. In response to high NaCl, many of its major processes, such as photosynthesi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1760-5
更新日期:2015-07-19 00:00:00
abstract:BACKGROUND:Increased focus surrounds identifying patients with advanced non-small cell lung cancer (NSCLC) who will benefit from treatment with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI). EGFR mutation, gene copy number, coexpression of ErbB proteins and ligands, and epithelial to mesenchy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-289
更新日期:2006-11-10 00:00:00
abstract:BACKGROUND:Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the pa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5214-8
更新日期:2018-11-29 00:00:00
abstract:BACKGROUND:Laboratory evolution is an important tool for developing robust yeast strains for bioethanol production since the biological basis behind combined tolerance requires complex alterations whose proper regulation is difficult to achieve by rational metabolic engineering. Previously, we reported on the evolved i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1737-4
更新日期:2015-07-09 00:00:00
abstract:BACKGROUND:Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi. To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, de...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-147
更新日期:2008-03-28 00:00:00
abstract:BACKGROUND:JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the geno...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5075-1
更新日期:2018-09-19 00:00:00
abstract:BACKGROUND:Three-dimensional (3D) multicellular spheroids of mesenchymal stem cells (MSCs) are generally regarded to have beneficial properties over MSCs in monolayer. Recent literatures have documented that MSCs can self-assemble into 3D spheroids with a greater capacity for differentiation into various cell types whe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-10
更新日期:2014-01-05 00:00:00